2018-07-23 14:14:03 +02:00
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context("bactid.R")
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test_that("as.bactid works", {
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expect_identical(
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as.character(as.bactid(c("E. coli", "H. influenzae"))),
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c("ESCCOL", "HAEINF"))
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expect_equal(as.character(as.bactid("Escherichia coli")), "ESCCOL")
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expect_equal(as.character(as.bactid("P. aer")), "PSEAER") # not Pasteurella aerogenes
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expect_equal(as.character(as.bactid("Negative rods")), "GNR")
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expect_equal(as.character(as.bactid("MRSE")), "STAEPI")
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expect_equal(as.character(as.bactid("VRE")), "ENC")
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expect_equal(as.character(as.bactid("MRPA")), "PSEAER")
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expect_equal(as.character(as.bactid("PISP")), "STCPNE")
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expect_equal(as.character(as.bactid("PRSP")), "STCPNE")
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expect_equal(as.character(as.bactid("VISP")), "STCPNE")
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expect_equal(as.character(as.bactid("VRSP")), "STCPNE")
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expect_identical(
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as.character(
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as.bactid(c("stau",
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"STAU",
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"staaur",
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"S. aureus",
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"S aureus",
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"Staphylococcus aureus",
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"MRSA",
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"VISA"))),
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rep("STAAUR", 8))
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# select with one column
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expect_identical(
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septic_patients[1:10,] %>%
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left_join_microorganisms() %>%
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select(genus) %>%
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as.bactid() %>%
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as.character(),
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2018-07-25 14:17:04 +02:00
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c("ESC", "ESC", "STA", "STA", "STA",
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"STA", "STA", "STA", "STA", "STA"))
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2018-07-23 14:14:03 +02:00
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# select with two columns
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expect_identical(
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septic_patients[1:10,] %>%
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pull(bactid),
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septic_patients[1:10,] %>%
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left_join_microorganisms() %>%
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select(genus, species) %>%
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as.bactid() %>%
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as.character())
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# unknown results
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expect_warning(as.bactid(c("INVALID", "Yeah, unknown")))
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# print
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expect_output(print(as.bactid(c("ESCCOL", NA))))
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# helper function
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expect_identical(as.bactid("ESCCOL"),
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guess_bactid("ESCCOL"))
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2018-07-29 22:14:51 +02:00
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# test pull
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expect_equal(nrow(septic_patients %>% mutate(bactid = as.bactid(bactid))),
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2000)
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# test data.frame
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expect_equal(nrow(data.frame(test = as.bactid("ESCCOL"))),
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1)
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2018-07-23 14:14:03 +02:00
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2018-07-30 00:14:06 +02:00
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# check empty values
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expect_equal(as.character(suppressWarnings(as.bactid(""))),
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NA_character_)
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2018-07-23 14:14:03 +02:00
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})
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